New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library !
BioRuby project
11 months
289
13
116265
0
0
Parser of scientific names !
Dmitry Mozzherin
9 months
23
3
68977
0
0
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
6 days
24
6
51144
7
19
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
2 years
15
12
48325
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
10 weeks
93
56
38333
0
25
Gadgets for bioinformatics
Shintaro Katayama
2 years
1
34380
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
2 years
16
1
32610
0
0
Http requests to entrez e-utilities
Jared Ning
13 months
6
1
30401
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
2 years
11
5
28017
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
4 years
18
5
27689
0
0
Maf parser for BioRuby
Clayton Wheeler
3 years
10
36
23830
0
0
Gff3 parser for big data !
Pjotr Prins
3 years
6
2
23186
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
13 months
12
1
21376
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
3 years
5
...
21000
0
0
Interfaces with biomodel search engine !
Niall Beard
4 years
1
...
20666
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
4 years
4
2
18769
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
9 months
2
1
18009
0
0
A simple obo file handler !
mjy
4 years
5
...
17723
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
17 months
12
3
17245
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
2 years
9
20
15142
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
2 years
8
5
14596
0
0
A fast parser for fastq files
Francesco Strozzi
3 years
10
...
14596
0
0
Data mining algorithms for jRuby
arrigonialberto86
2 years
15
3
14501
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
3 years
12266
0
0
Low memory sequence emitters
Pjotr Prins
2 years
11
1
11792
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
4 years
2
1
11695
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
22 months
3
...
11266
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
5 years
1
...
11052
0
0
Build genome output files
Michael Barton
2 years
5
...
10851
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
3 years
5
...
10454
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
3 years
2
...
10217
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
3 years
30
15
10106
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
5 years
4
...
10025
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
4 years
1
...
10024
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
4 months
33
8
9946
0
29
Ruby wrapper for sambamba tool
Artem Tarasov
3 years
2
...
9886
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
2 years
8
...
9644
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
4 years
8
2
9484
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
4 years
3
...
9473
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
2 years
...
9197
0
1
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
2 weeks
8705
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
2 years
13
2
8638
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
8 years
21
1
8447
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
5 years
4
...
8402
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
3 years
3
...
8078
0
0
Parser to work with file formats used in
Ben J Woodcroft
16 months
...
7933
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
5 years
1
...
7684
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
15 months
...
7684
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
5 years
4
...
7030
0
0
Read and manipulate cd-hit clusters
George Githinji
3 years
7008
0
0
Ruby binding for samtools tabix
throwern
2 years
5
...
6831
0
0
A plugin that allows you to parse large
robsyme
5 years
1
...
6785
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
5 years
10
...
6595
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
3 years
2
...
6571
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
5 years
41
5
6117
0
0
A general purpose framework for scripted handling of development/stable
mjy
3 years
2
1
5897
0
4
Ruby wrapper for the gff3-pltools
Marjan Povolni
3 years
13
19
5821
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
3 years
1
1
5719
0
0
Next-generation mapping of mutations
Dan MacLean
3 years
2
...
5688
0
0
Ruby binding to the ucsc kent utilities
throwern
3 years
2
...
5652
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
6 weeks
1
...
5515
0
11
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
9 months
5513
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
2 years
5488
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
4 weeks
1
...
5433
0
0
Publish scientific results to the semantic web !
Will Strinz
24 months
3
16
5300
0
0
Bioinformatics triple-store support
Pjotr Prins
4 years
4
1
5270
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
4 years
2
1
5238
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
5 years
1
...
5232
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
5 months
1
...
5189
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
3 years
4880
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
3 years
...
4777
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
16 months
1
4728
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
4 years
1
...
4633
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
4 years
2
...
4450
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
4 years
1
...
4437
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
2 years
1
...
4330
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
4 years
1
...
4051
0
0
A protparam compatible utility for BioRuby
hryk
3 years
2
...
3988
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
3 years
2
...
3883
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
6 weeks
...
3773
0
2
Ruby parser for fastqc output
Tazro Inutano Ohta
5 days
2
...
3571
3
54
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
8 months
1
...
3528
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
19 months
1
3290
0
0
Biostars data-mining and statistical analysis
Joachim Baran
2 years
3267
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
9 months
2
1
3113
0
0
Gggenome Ruby client
Mitsuteru Nakao
2 years
1
...
2942
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
7 years
5
...
2898
0
0
Ruby ensembl rest api
Alberto Donizetti
2 years
3
...
2883
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
2 years
6
...
2854
0
0
Generalized linear models for statsample
Ankur Goel
2 years
2761
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
5 years
3
...
2743
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
5 years
4
...
2729
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
8 months
2
1
2718
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
4 years
1
2695
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
6 years
1
...
2625
0
0
Interface for express beta diversity
Ben J. Woodcroft
2 years
...
2557
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
5 years
1
...
2510
0
0
Bio-repeatmasker
Andrei Rozanski
2 years
...
2499
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
5 months
2
...
2480
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
4 years
1
...
2449
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
4 years
2
...
2436
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
4 years
4
...
2425
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
4 years
...
2410
0
0
One-line summary of your gem
Toshiaki Katayama
4 years
1
...
2399
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
4 years
1
...
2384
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
3 weeks
13
6
2376
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
4 years
4
...
2369
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
4 years
3
1
2353
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
4 years
1
...
2351
0
0
A parser for cigar format alignments
Ben J Woodcroft
2 years
4
...
2343
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
4 years
1
...
2342
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
4 years
1
...
2320
0
0
Web server for bio-samtools
homonecloco
2 years
...
2266
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
3 years
3
...
2180
0
0
Build graph with jRuby
Matteo Picciolini
3 years
2151
0
0
Helper methods for reading .delta files
robsyme
14 months
...
2143
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
7 years
89
1
2021
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
3 years
...
1894
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
2 years
2
...
1710
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
3 months
3
...
1645
0
2
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
2 years
...
1628
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
11 months
...
1403
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
12 months
1351
0
0
Mine publications for gene names
Pjotr Prins
2 years
...
1252
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
22 months
1
...
1174
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
2 years
1149
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
20 months
1
...
1128
0
0
Tools to work with fasta files, indexed with
homonecloco
20 months
...
1072
0
0
Tools to manipulate blat files from the command
homonecloco
20 months
...
1049
0
0
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
18 months
...
1021
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
18 months
...
1014
0
0
Api of picard tool
Natapol Pornputtapong
12 months
926
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
7 years
897
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
9 months
638
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
8 months
...
619
0
0
Basic wrapper for the kallistio mapper
homonecloco
7 months
1
...
599
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
13 months
444
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
4 months
...
438
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
3 months
...
376
0
0
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2016-05-31
**) number of commits on GitHub (last 7 days & last 90 days)